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comparison heatmapper.xml @ 39:c6f1a059bc7d

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author bgruening
date Fri, 02 Aug 2013 12:18:55 -0400
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38:1a78aa9ea234 39:c6f1a059bc7d
1 <tool id="heatmapper" name="Heatmapper" version="1.0">
2 <description>creates a heatmap for a score associated to genomic regions</description>
3
4 <requirements>
5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="1.7.1">numpy</requirement>
7 <requirement type="package" version="1.2.1">matplotlib</requirement>
8 <requirement type="package" version="0.12.0">scipy</requirement>
9 <requirement type="package" version="0.1">ucsc_tools</requirement>
10 <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
11 </requirements>
12
13 <command>
14 heatmapper
15 --matrixFile $matrixFile
16 #if $output.showOutputSettings == "yes"
17 #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
18 --outFileName $newoutFileName
19 #if $outFileNameData:
20 --outFileNameData '$outFileNameData'
21 #end if
22
23 #if $outFileNameMatrix:
24 --outFileNameMatrix '$outFileNameMatrix'
25 #end if
26
27 #if $outFileSortedRegions:
28 --outFileSortedRegions '$outFileSortedRegions'
29 #end if
30 #else
31 #set newoutFileName=str($outFileName)+".png"
32 --outFileName $newoutFileName
33 #end if
34
35 #if $advancedOpt.showAdvancedOpt == "yes"
36 #if $advancedOpt.sortRegions:
37 --sortRegions '$advancedOpt.sortRegions'
38 #end if
39
40 #if $advancedOpt.sortUsing:
41 --sortUsing '$advancedOpt.sortUsing'
42 #end if
43
44 #if $advancedOpt.averageTypeSummaryPlot:
45 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
46 #end if
47
48 #if str($advancedOpt.missingDataColor.value) != "None":
49 --missingDataColor '$advancedOpt.missingDataColor'
50 #end if
51
52 --colorMap '$advancedOpt.colorMap'
53
54 #if $advancedOpt.zMin:
55 --zMin $advancedOpt.zMin
56 #end if
57 #if $advancedOpt.zMax:
58 --zMax $advancedOpt.zMax
59 #end if
60
61 #if $advancedOpt.yMin:
62 --yMin $advancedOpt.yMin
63 #end if
64 #if $advancedOpt.yMax:
65 --yMax $advancedOpt.yMax
66 #end if
67
68 --xAxisLabel '$advancedOpt.xAxisLabel'
69 --yAxisLabel '$advancedOpt.yAxisLabel'
70
71 --heatmapWidth $advancedOpt.heatmapWidth
72 --heatmapHeight $advancedOpt.heatmapHeight
73
74 --whatToShow '$advancedOpt.whatToShow'
75
76 --startLabel '$advancedOpt.startLabel'
77 --endLabel '$advancedOpt.endLabel'
78 --refPointLabel '$advancedOpt.referencePointLabel'
79 --regionsLabel '$advancedOpt.regionsLabel'
80
81 #if str($advancedOpt.plotTitle.value) != "None":
82 --plotTitle '$advancedOpt.plotTitle'
83 #end if
84
85 $advancedOpt.onePlotPerGroup
86 #end if
87 ; mv $newoutFileName $outFileName
88 </command>
89 <inputs>
90 <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
91
92 <conditional name="output" >
93 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
94 <option value="no" selected="true">no</option>
95 <option value="yes">yes</option>
96 </param>
97 <when value="no" />
98 <when value="yes">
99 <param name="outFileFormat" type="select" label="Image file format">
100 <option value="png" selected="true">png</option>
101 <option value="pdf">pdf</option>
102 <option value="svg">svg</option>
103 <option value="eps">eps</option>
104 <option value="emf">emf</option>
105 </param>
106 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
107 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
108 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
109 </when>
110 </conditional>
111
112 <conditional name="advancedOpt" >
113 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
114 <option value="no" selected="true">no</option>
115 <option value="yes">yes</option>
116 </param>
117 <when value="no" />
118 <when value="yes">
119 <param name="sortRegions" type="select" label="Sort regions"
120 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
121 <option value="no" selected="true">no ordering</option>
122 <option value="descend">descending order</option>
123 <option value="ascend">ascending order</option>
124 </param>
125
126 <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
127 <option value="mean" selected="true">mean</option>
128 <option value="median">median</option>
129 <option value="min">min</option>
130 <option value="max">max</option>
131 <option value="sum">sum</option>
132 <option value="region_length">region length</option>
133 </param>
134
135 <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
136 <option value="mean" selected="true">mean</option>
137 <option value="median">median</option>
138 <option value="min">min</option>
139 <option value="max">max</option>
140 <option value="sum">sum</option>
141 <option value="std">std</option>
142 </param>
143
144 <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." />
145
146 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available values can be seen here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
147 <option value="RdYlBu" selected="true">RdYlBu</option>
148 <option value="Accent">Accent</option>
149 <option value="Spectral">Spectral</option>
150 <option value="Set1">Set1</option>
151 <option value="Set2">Set2</option>
152 <option value="Set3">Set3</option>
153 <option value="Dark2">Dark2</option>
154 <option value="Reds">Reds</option>
155 <option value="Oranges">Oranges</option>
156 <option value="Greens">Greens</option>
157 <option value="Blues">Blues</option>
158 <option value="Greys">Greys</option>
159 <option value="Purples">Purples</option>
160 <option value="Paired">Paired</option>
161 <option value="Pastel1">Pastel1</option>
162 <option value="Pastel2">Pastel2</option>
163 <option value="spring">spring</option>
164 <option value="summer">summer</option>
165 <option value="autumn">autumn</option>
166 <option value="winter">winter</option>
167 <option value="hot">hot</option>
168 <option value="coolwarm">coolwarm</option>
169 <option value="cool">cool</option>
170 <option value="seismic">seismic</option>
171 <option value="terrain">terrain</option>
172 <option value="ocean">ocean</option>
173 <option value="rainbow">rainbow</option>
174 <option value="bone">bone</option>
175 <option value="flag">flag</option>
176 <option value="prism">prism</option>
177 <option value="cubehelix">cubehelix</option>
178 <option value="binary">binary</option>
179 <option value="pink">pink</option>
180 <option value="gray">gray</option>
181 <option value="copper">copper</option>
182 <option value="BrBG">BrBG</option>
183 <option value="BuGn">BuGn</option>
184 <option value="BuPu">BuPu</option>
185 <option value="GnBu">GnBu</option>
186 <option value="OrRd">OrRd</option>
187 <option value="PiYG">PiYG</option>
188 <option value="PRGn">PRGn</option>
189 <option value="PuOr">PuOr</option>
190 <option value="PuRd">PuRd</option>
191 <option value="PuBu">PuBu</option>
192 <option value="RdBu">RdBu</option>
193 <option value="RdGy">RdGy</option>
194 <option value="RdPu">RdPu</option>
195 <option value="YlGn">YlGn</option>
196 <option value="PuBuGn">PuBuGn</option>
197 <option value="RdYlGn">RdYlGn</option>
198 <option value="YlGnBu">YlGnBu</option>
199 <option value="YlOrBr">YlOrBr</option>
200 <option value="YlOrRd">YlOrRd</option>
201 <option value="gist_gray">gist_gray</option>
202 <option value="gist_stern">gist_stern</option>
203 <option value="gist_earth">gist_earth</option>
204 <option value="gist_yarg">gist_yarg</option>
205 <option value="gist_ncar">gist_ncar</option>
206 <option value="gist_rainbow">gist_rainbow</option>
207 <option value="gist_heat">gist_heat</option>
208 <option value="gnuplot">gnuplot</option>
209 <option value="gnuplot2">gnuplot2</option>
210 <option value="CMRmap">CMRmap</option>
211 <option value="bwr">bwr</option>
212 <option value="hsv">hsv</option>
213 <option value="brg">brg</option>
214 <option value="jet">jet</option>
215 <option value="afmhot">afmhot</option>
216
217 <option value="Accent_r">Accent reversed</option>
218 <option value="Spectral_r">Spectral reversed</option>
219 <option value="Set1_r">Set1 reversed</option>
220 <option value="Set2_r">Set2 reversed</option>
221 <option value="Set3_r">Set3 reversed</option>
222 <option value="Dark2_r">Dark2 reversed</option>
223 <option value="Reds_r">Reds reversed</option>
224 <option value="Oranges_r">Oranges reversed</option>
225 <option value="Greens_r">Greens reversed</option>
226 <option value="Blues_r">Blues reversed</option>
227 <option value="Greys_r">Greys reversed</option>
228 <option value="Purples_r">Purples reversed</option>
229 <option value="Paired_r">Paired reversed</option>
230 <option value="Pastel1_r">Pastel1 reversed</option>
231 <option value="Pastel2_r">Pastel2 reversed</option>
232 <option value="spring_r">spring reversed</option>
233 <option value="summer_r">summer reversed</option>
234 <option value="autumn_r">autumn reversed</option>
235 <option value="winter_r">winter reversed</option>
236 <option value="hot_r">hot reversed</option>
237 <option value="coolwarm_r">coolwarm reversed</option>
238 <option value="cool_r">cool reversed</option>
239 <option value="seismic_r">seismic reversed</option>
240 <option value="terrain_r">terrain reversed</option>
241 <option value="ocean_r">ocean reversed</option>
242 <option value="rainbow_r">rainbow reversed</option>
243 <option value="bone_r">bone reversed</option>
244 <option value="flag_r">flag reversed</option>
245 <option value="prism_r">prism reversed</option>
246 <option value="cubehelix_r">cubehelix reversed</option>
247 <option value="binary_r">binary reversed</option>
248 <option value="pink_r">pink reversed</option>
249 <option value="gray_r">gray reversed</option>
250 <option value="copper_r">copper reversed</option>
251 <option value="BrBG_r">BrBG reversed</option>
252 <option value="BuGn_r">BuGn reversed</option>
253 <option value="BuPu_r">BuPu reversed</option>
254 <option value="GnBu_r">GnBu reversed</option>
255 <option value="OrRd_r">OrRd reversed</option>
256 <option value="PiYG_r">PiYG reversed</option>
257 <option value="PRGn_r">PRGn reversed</option>
258 <option value="PuOr_r">PuOr reversed</option>
259 <option value="PuRd_r">PuRd reversed</option>
260 <option value="PuBu_r">PuBu reversed</option>
261 <option value="RdBu_r">RdBu reversed</option>
262 <option value="RdGy_r">RdGy reversed</option>
263 <option value="RdPu_r">RdPu reversed</option>
264 <option value="YlGn_r">YlGn reversed</option>
265 <option value="PuBuGn_r">PuBuGn reversed</option>
266 <option value="RdYlBu_r">RdYlBu reversed</option>
267 <option value="RdYlGn_r">RdYlGn reversed</option>
268 <option value="YlGnBu_r">YlGnBu reversed</option>
269 <option value="YlOrBr_r">YlOrBr reversed</option>
270 <option value="YlOrRd_r">YlOrRd reversed</option>
271 <option value="gist_gray_r">gist_gray reversed</option>
272 <option value="gist_stern_r">gist_stern reversed</option>
273 <option value="gist_earth_r">gist_earth reversed</option>
274 <option value="gist_yarg_r">gist_yarg reversed</option>
275 <option value="gist_ncar_r">gist_ncar reversed</option>
276 <option value="gist_rainbow_r">gist_rainbow reversed</option>
277 <option value="gist_heat_r">gist_heat reversed</option>
278 <option value="gnuplot_r">gnuplot reversed</option>
279 <option value="gnuplot2_r">gnuplot2 reversed</option>
280 <option value="CMRmap_r">CMRmap reversed</option>
281 <option value="bwr_r">bwr reversed</option>
282 <option value="hsv_r">hsv reversed</option>
283 <option value="brg_r">brg reversed</option>
284 <option value="jet_r">jet reversed</option>
285 <option value="afmhot_r">afmhot reversed</option>
286 </param>
287
288 <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
289 <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
290 <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
291 <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
292
293 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" />
294 <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" />
295
296 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
297
298 <param name="heatmapHeight" type="float" value="25" min="3" max="100" label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
299
300 <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
301 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
302 <option value="plot only">summary plot only</option>
303 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
304 <option value="heatmap only">heatmap only</option>
305 <option value="heatmap and colorbar">heatmap and colorbar</option>
306 <option value="colorbar only">colorbar only</option>
307 </param>
308
309 <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
310 <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
311
312 <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
313
314 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
315
316 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
317
318 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
319
320
321 </when>
322 </conditional>
323
324 </inputs>
325 <outputs>
326 <data format="png" name="outFileName" label="${tool.name} image">
327 <change_format>
328 <when input="output.outFileFormat" value="pdf" format="pdf" />
329 <when input="output.outFileFormat" value="svg" format="svg" />
330 <when input="output.outFileFormat" value="eps" format="eps" />
331 <when input="output.outFileFormat" value="emf" format="emf" />
332 </change_format>
333 </data>
334 <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
335 <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
336 </data>
337 <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
338 <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
339 </data>
340 <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
341 <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
342 </data>
343 </outputs>
344
345 <help>
346
347 **What it does**
348
349 HeatMapper visualizes scores associated with genomic regions, for example log2 fold change values obtained from ChIP-seq experiments. Those values can be visualized individually along each of the regions provided by the user.
350
351 -----
352
353 .. class:: infomark
354
355 Please acknowledge that this tool **is still in development** and we will be very happy to receive feedback from the users. If you run into any trouble please sent an email to `Fidel Ramirez`_.
356
357 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
358
359
360 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
361 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
362 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
363 </help>
364
365 </tool>